I finally got to the bottom of my issue. It's the ' color.branch'
variable that causes the trouble for the bash script. Because I had
explicitly set it to 'always' in my '~/.gitconfig' file, `git branch -r
` command append the wierd control characters to the release branch
name, e.g. 'release-3
Thank you Jim for your reply.
SubGit does highlight its ability to handle non-linear histories as
compared to GitSVN -- http://www.subgit.com/documentation/gitsvn.html.
I will keep looking as well.
Thanks.
On Wed, Jul 15, 2015 at 9:03 AM Jim Hester wrote:
> Sid,
>
> I think you have character
Sid,
I think you have characterized the main issue well, a number of people have
run into issues stemming from the same problem. (
https://stat.ethz.ch/pipermail/bioc-devel/2015-June/007726.html,
https://stat.ethz.ch/pipermail/bioc-devel/2015-June/007730.html and a
number of off-list queries).
As
[cc]: bioc-devel for discussion with wider community.
Hello Jim!
This is related to using the new git mirror setup with pre-existing github
repos (not forks of the mirror).
I tried following the thread on
https://stat.ethz.ch/pipermail/bioc-devel/2015-June/007725.html but it
looks like the probl
emotes.sh
> git checkout devel
> git svn rebase
>
> Dan
>
> - Original Message -
> > From: "Guangchuang Yu"
> > To: "Dan Tenenbaum"
> > Cc: bioc-devel@r-project.org
> > Sent: Monday, June 22, 2015 6:02:25 AM
> > Subject: Re
b.com/GuangchuangYu/GOSemSim
cd GOSemSim
bash ../mirror/update_remotes.sh
git checkout devel
git svn rebase
Dan
- Original Message -
> From: "Guangchuang Yu"
> To: "Dan Tenenbaum"
> Cc: bioc-devel@r-project.org
> Sent: Monday, June 22, 2015 6:02:25 AM
> Su
gchuang
On Sat, Jun 20, 2015 at 2:27 AM, Dan Tenenbaum
wrote:
>
>
> - Original Message -
> > From: "Guangchuang Yu"
> > To: bioc-devel@r-project.org
> > Sent: Wednesday, June 17, 2015 5:04:04 AM
> > Subject: Re: [Bioc-devel] Bioconductor Git/Gi
; > From: "davide risso"
> > To: "Leonardo Collado Torres" , "Dan Tenenbaum" <
> dtene...@fredhutch.org>, "Jim Hester"
> >
> > Cc: bioc-devel@r-project.org
> > Sent: Friday, June 19, 2015 8:07:29 PM
> > Subject: Re: [Bi
- Original Message -
> From: "davide risso"
> To: "Leonardo Collado Torres" , "Dan Tenenbaum"
> , "Jim Hester"
>
> Cc: bioc-devel@r-project.org
> Sent: Friday, June 19, 2015 8:07:29 PM
> Subject: Re: [Bioc-devel] Bioconducto
> git svn rebase
> git merge master
> git svn dcommit --add-author-from
>
>
>
> Or it did work partially since
>
> https://github.com/Bioconductor-mirror/derfinderHelper/commit/402100dc8d78ccbb99a4d65dc6f748fb7474a69d
> does not include the message from
>
> http
git svn dcommit --add-author-from
git svn rebase
## For each conflict loop, do
grep -lr '<<<<<<<' . | xargs git checkout --theirs
git add *
git rebase --continue
## Once that's done, do
git svn dcommit --add-author-from
## Then pull from the Bioc mirror
git
Mike,
We are unable to reproduce this issue using the commands provided. Maybe
try starting over from scratch and see if it works, perhaps there was a
network error the first time you tried it?
Jim
On Fri, Jun 19, 2015 at 3:03 PM, Mike wrote:
> I am having trouble to set up the remote.
>
> gi
I am having trouble to set up the remote.
git clone https://github.com/RGLab/flowQ
cd flowQ/
git branch -a
* master
remotes/origin/HEAD -> origin/master
remotes/origin/master
curl -O
https://raw.githubusercontent.com/Bioconductor/mirror/master/update_remotes.sh
bash update_remotes.sh
fatal
- Original Message -
> From: "Guangchuang Yu"
> To: bioc-devel@r-project.org
> Sent: Wednesday, June 17, 2015 5:04:04 AM
> Subject: Re: [Bioc-devel] Bioconductor Git/GitHub Mirrors
>
> Dear Dan,
>
> I update my package
> GOSemSim(https://github.co
Hmmm, ok. I kind of liked having the message about being a fork of the
Bioc-mirror, but the difference message makes it a little messy. Oh well.
Was an interesting experiment.
On Fri, Jun 19, 2015 at 11:19 AM Jim Hester
wrote:
> I think these are unavoidable artifacts with the current setup. Th
I think these are unavoidable artifacts with the current setup. The
commits from the Bioconductor-mirror are coming from SVN after being
translated so they have extra metadata attached to the commit message,
while your original commits do not have this. Therefore GitHub cannot
properly disambigua
So this seems to work quite nicely. But in my own testing of committing
with my categoryCompare package, there is one interesting issue of Github
complaining about how many commits ahead / behind the fork is.
So I moved my old github repo, and then made a fresh fork from the
Bioconductor mirror, a
I have (in the past couple of minutes) added a more detailed description to
all of the GitHub pages. If you have URL or BugReports fields in your
package DESCRIPTION those are used to provide links to the project page and
bug tracker if they are available, see Roberts
https://github.com/Bioconduct
Why not write your own *readme.md* file for the package and put the link
there? There is nothing stopping the maintainer from having a README file
in the package. Although it does not show up on the Bioconductor page, it
shows up nicely on Github:
My package:
https://github.com/Bioconductor-mirro
It would be cool if we could somehow get the equivalent of the
bioconductor package page to show up as the "readme" on the github
page. Or at least, if there could be a very obvious link from the
mirror repository to the maintainer repository, without having to
click through to the Bioconductor pac
Dear Dan,
I update my package GOSemSim(https://github.com/GuangchuangYu/GOSemSim),
with the following steps:
1. delete the git-svn-bridge
1. bash /path/to/update_remotes.sh
2. git checkout devel
3. git checkout master
4. git merge devel
All was fine without any error.
But when I follow the in
- Original Message -
> From: "Dan Tenenbaum"
> To: "Leonardo Collado Torres"
> Cc: "bioc-devel"
> Sent: Tuesday, June 16, 2015 8:10:56 PM
> Subject: Re: [Bioc-devel] Bioconductor Git/GitHub Mirrors
>
>
>
> - Original M
On Tue, Jun 16, 2015 at 10:02 PM, Dan Tenenbaum wrote:
>
>
> - Original Message -
>> From: "Leonardo Collado Torres"
>> To: "Ryan C. Thompson"
>> Cc: "Dan Tenenbaum" , "bioc-devel"
>>
>> Sent: Tuesday
- Original Message -
> From: "Dan Tenenbaum"
> To: "Leonardo Collado Torres"
> Cc: "bioc-devel"
> Sent: Tuesday, June 16, 2015 8:05:37 PM
> Subject: Re: [Bioc-devel] Bioconductor Git/GitHub Mirrors
>
>
>
> - Original M
- Original Message -
> From: "Dan Tenenbaum"
> To: "Leonardo Collado Torres"
> Cc: "bioc-devel" , "Ryan C. Thompson"
>
> Sent: Tuesday, June 16, 2015 7:02:36 PM
> Subject: Re: [Bioc-devel] Bioconductor Git/GitHub Mirrors
&
- Original Message -
> From: "Leonardo Collado Torres"
> To: "Ryan C. Thompson"
> Cc: "Dan Tenenbaum" , "bioc-devel"
>
> Sent: Tuesday, June 16, 2015 5:55:05 PM
> Subject: Re: [Bioc-devel] Bioconductor Git/GitHub Mirrors
&
- Original Message -
> From: "Leonardo Collado Torres"
> To: "Ryan C. Thompson"
> Cc: "Dan Tenenbaum" , "bioc-devel"
>
> Sent: Tuesday, June 16, 2015 5:55:05 PM
> Subject: Re: [Bioc-devel] Bioconductor Git/GitHub Mirrors
&
On Tue, Jun 16, 2015 at 8:55 PM, Leonardo Collado Torres
wrote:
> Hi,
>
>
> This sounds great! Not having to setup all those bridges everytime a
> new BioC version is released should be a great feature, plus keeping
> the commit history tidy. And we can still use Travis or other things
> like Slac
Hi,
This sounds great! Not having to setup all those bridges everytime a
new BioC version is released should be a great feature, plus keeping
the commit history tidy. And we can still use Travis or other things
like Slack notifications on our own bridges. I guess that it'd be good
to remind users
This is great to hear. I sometimes want to delve into the source code of
a package's internals, but doing so through the SVN web interface is
clunky. Being able to use Github's repo browsing functionality for Bioc
packages is great.
On 06/16/2015 12:00 PM, Dan Tenenbaum wrote:
Dear Bioconduct
Correct link is http://bioconductor.org/developers/how-to/git-mirrors/
On Tue, Jun 16, 2015 at 3:00 PM Dan Tenenbaum
wrote:
> Dear Bioconductors,
>
> We're pleased to announce the availability of Bioconductor Git Mirrors.
> These are read-only GitHub repositories (available under
> https://githu
Dear Bioconductors,
We're pleased to announce the availability of Bioconductor Git Mirrors.
These are read-only GitHub repositories (available under
https://github.com/Bioconductor-mirror)
for every Bioconductor software package. These repositories are synchronized
with our
Subversion reposit
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